Pacification states that you are "unable to use Weapon Skills". This is a bit vague, but if you have ever used Berserk on WAR, you'll notice that even though you can't use anything on GCD, you can use Off-GCD abilities, like Brutal Swing. Therefore, I would guess that some abilities simply aren't considered "Weapon Skills" when being used by you or enemies. That almost definitely includes caster abilities, such as Fire or Blizzard.

Later on, a lot of enemies fully resist Pacification, so it is still kind of hard to tell the specifics.